MetaDataBrowser.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Marc Sturm $
// --------------------------------------------------------------------------

#pragma once

// OpenMS_GUI config
#include <OpenMS/VISUAL/OpenMS_GUIConfig.h>

#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/KERNEL/ConsensusMap.h>

//QT
#include <QtWidgets/QDialog>
#include <QtWidgets/QTreeWidget>
class QTreeWidgetItem;
class QPushButton;
class QStackedWidget;
class QHBoxLayout;
class QVBoxLayout;
class QGridLayout;

namespace OpenMS
{
  class BaseVisualizerGUI;
  class Acquisition;
  class AcquisitionInfo;
  class ContactPerson;
  class Digestion;
  class ExperimentalSettings;
  class Gradient;
  class HPLC;
  class PeptideIdentification;
  class Instrument;
  class IonDetector;
  class IonSource;
  class MassAnalyzer;
  class MetaInfo;
  class MetaInfoDescription;
  class MetaInfoInterface;
  class MetaInfoRegistry;
  class Modification;
  class PeptideHit;
  class Precursor;
  class DataProcessing;
  class ProteinHit;
  class ProteinIdentification;
  class Sample;
  class SampleTreatment;
  class Software;
  class SourceFile;
  class SpectrumSettings;
  class Tagging;
  class DocumentIdentifier;
  class Product;

  class OPENMS_GUI_DLLAPI MetaDataBrowser :
    public QDialog
  {
    Q_OBJECT

public:

    MetaDataBrowser(bool editable = false, QWidget * parent = nullptr, bool modal = false);

    void add(PeakMap & exp)
    {
      add(static_cast<ExperimentalSettings &>(exp));
      treeview_->expandItem(treeview_->findItems(QString::number(0), Qt::MatchExactly, 1).first());
    }

    void add(MSSpectrum & spectrum)
    {
      //spectrum settings
      add(static_cast<SpectrumSettings &>(spectrum));

      //MetaInfoDescriptions
      for (Size i = 0; i < spectrum.getFloatDataArrays().size(); ++i)
      {
        add(spectrum.getFloatDataArrays()[i]);
      }
      for (Size i = 0; i < spectrum.getIntegerDataArrays().size(); ++i)
      {
        add(spectrum.getIntegerDataArrays()[i]);
      }
      for (Size i = 0; i < spectrum.getStringDataArrays().size(); ++i)
      {
        add(spectrum.getStringDataArrays()[i]);
      }

      add(static_cast<MetaInfoInterface &>(spectrum));

      treeview_->expandItem(treeview_->findItems(QString::number(0), Qt::MatchExactly, 1).first());
    }

    void add(FeatureMap& map)
    {
      //identifier
      add(static_cast<DocumentIdentifier &>(map));

      //protein ids
      for (Size i = 0; i < map.getProteinIdentifications().size(); ++i)
      {
        add(map.getProteinIdentifications()[i]);
      }

      //unassigned peptide ids
      for (Size i = 0; i < map.getUnassignedPeptideIdentifications().size(); ++i)
      {
        add(map.getUnassignedPeptideIdentifications()[i]);
      }

      treeview_->expandItem(treeview_->findItems(QString::number(0), Qt::MatchExactly, 1).first());
    }

    void add(Feature & feature);
    void add(ConsensusFeature & feature);

    void add(ConsensusMap & map);

    template <class MetaDataType>
    void add(MetaDataType & meta_data_object)
    {
      visualize_(meta_data_object);
      treeview_->expandItem(treeview_->findItems(QString::number(0), Qt::MatchExactly, 1).first());
    }

    bool isEditable();

    friend class ProteinIdentificationVisualizer;
    friend class PeptideIdentificationVisualizer;

public slots:

    void setStatus(std::string status);

protected slots:

    void showDetails_();

    void saveAll_();

protected:


    void visualize_(ExperimentalSettings & meta, QTreeWidgetItem * parent = nullptr);
    void visualize_(SpectrumSettings & meta, QTreeWidgetItem * parent = nullptr);
    void visualize_(MetaInfoInterface & meta, QTreeWidgetItem * parent = nullptr);
    void visualize_(Sample & meta, QTreeWidgetItem * parent = nullptr);
    void visualize_(HPLC & meta, QTreeWidgetItem * parent = nullptr);
    void visualize_(Digestion & meta, QTreeWidgetItem * parent = nullptr);
    void visualize_(Modification & meta, QTreeWidgetItem * parent = nullptr);
    void visualize_(Tagging & meta, QTreeWidgetItem * parent = nullptr);
    void visualize_(Gradient & meta, QTreeWidgetItem * parent = nullptr);
    void visualize_(Software & meta, QTreeWidgetItem * parent = nullptr);
    void visualize_(ScanWindow & meta, QTreeWidgetItem * parent = nullptr);
    void visualize_(SourceFile & meta, QTreeWidgetItem * parent = nullptr);
    void visualize_(ContactPerson & meta, QTreeWidgetItem * parent = nullptr);
    void visualize_(Instrument & meta, QTreeWidgetItem * parent = nullptr);
    void visualize_(IonSource & meta, QTreeWidgetItem * parent = nullptr);
    void visualize_(IonDetector & meta, QTreeWidgetItem * parent = nullptr);
    void visualize_(MassAnalyzer & meta, QTreeWidgetItem * parent = nullptr);
    void visualize_(DataProcessingPtr & meta, QTreeWidgetItem * parent = nullptr);
    void visualize_(ProteinIdentification & meta, QTreeWidgetItem * parent = nullptr);
    void visualize_(ProteinHit & meta, QTreeWidgetItem * parent = nullptr);
    void visualize_(PeptideHit & meta, QTreeWidgetItem * parent = nullptr);
    void visualize_(Acquisition & meta, QTreeWidgetItem * parent = nullptr);
    void visualize_(AcquisitionInfo & meta, QTreeWidgetItem * parent = nullptr);
    void visualize_(MetaInfoDescription & meta, QTreeWidgetItem * parent = nullptr);
    void visualize_(Precursor & meta, QTreeWidgetItem * parent = nullptr);
    void visualize_(Product & meta, QTreeWidgetItem * parent = nullptr);
    void visualize_(InstrumentSettings & meta, QTreeWidgetItem * parent = nullptr);
    void visualize_(PeptideIdentification & meta, QTreeWidgetItem * parent = nullptr);
    void visualize_(DocumentIdentifier & meta, QTreeWidgetItem * parent = nullptr);

    template <typename ContainerType>
    void visualizeAll_(ContainerType & container, QTreeWidgetItem * parent)
    {
      for (typename ContainerType::iterator it = container.begin(); it != container.end(); ++it)
      {
        visualize_(*it, parent);
      }
    }

    void connectVisualizer_(BaseVisualizerGUI * ptr);

    void filterHits_(double threshold, bool higher_better, int tree_item_id);
    void showAllHits_(int tree_item_id);

    std::string status_list_;

    bool editable_;

    QStackedWidget * ws_;
    QPushButton * saveallbutton_;
    QPushButton * closebutton_;
    QPushButton * cancelbutton_;
    QPushButton * undobutton_;

    QTreeWidget * treeview_;
  };
}